Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_068174237.1 HTA01S_RS18580 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_001592305.1:WP_068174237.1 Length = 432 Score = 540 bits (1390), Expect = e-158 Identities = 266/422 (63%), Positives = 324/422 (76%) Query: 3 SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62 +N LM RR AIPRGVGQ H IF + EN VWDVEGR Y+DFAGGIAVLNTGH +P V Sbjct: 8 TNAMLMARRQAAIPRGVGQSHAIFIAKGENAEVWDVEGRRYIDFAGGIAVLNTGHRNPAV 67 Query: 63 VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122 + AV+AQL + +HTCFQVLAYEPY+EL E +N K PGDFAKKTL +TTG+EAVENA+KIA Sbjct: 68 IEAVKAQLDQYTHTCFQVLAYEPYVELAERLNAKAPGDFAKKTLFLTTGAEAVENAIKIA 127 Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182 RA T R+G IAF+G YHGRT TL LTGKV PY G G PG ++ A +P LHG+S D Sbjct: 128 RAHTGRAGVIAFTGGYHGRTLMTLGLTGKVAPYKTGFGPFPGEIFHARFPNALHGVSVQD 187 Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242 AI S+ +IFKND +AAI+IEPVQGEGGF + P MQRLRALCD+HGI+L+ DEVQ Sbjct: 188 AIDSVEQIFKNDIEARRVAAIIIEPVQGEGGFNVAPPELMQRLRALCDQHGILLVCDEVQ 247 Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302 +GAGRTGT FA EQ GVAPDL T AKS+AGGFP++ V GRAEVMDA A GGLGGTYAG+P Sbjct: 248 TGAGRTGTWFACEQTGVAPDLITLAKSMAGGFPISAVVGRAEVMDAPAAGGLGGTYAGSP 307 Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362 +AC AAL VL FE+ +LLQ++ D+GQ++ L A+A+KH I DVRGLGAM+A+EL ++ Sbjct: 308 LACAAALAVLDEFEKHDLLQRSRDVGQRITASLQALAKKHKCIADVRGLGAMVAMELCKN 367 Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422 GD ++PDA LT + A A +GL++L+CG Y NV+RILVPLT+ DA + +GL II + Sbjct: 368 GDPHQPDADLTKALAAEATKRGLVILTCGTYGNVVRILVPLTVSDAVLDEGLAIIGASLE 427 Query: 423 EA 424 A Sbjct: 428 AA 429 Lambda K H 0.320 0.137 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 619 Number of extensions: 23 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 432 Length adjustment: 32 Effective length of query: 394 Effective length of database: 400 Effective search space: 157600 Effective search space used: 157600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory